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Introduction to Part 1
INTRODUCTION TO PART 1
Because all biochemical reactions involve energy changes, the term bioenergetics could validly be applied to the whole of life sciences. However, in the field of biochemistry and biology, the term originally came to mean the study of the energy conversion processes that occur on, in, or across the inner mitochondrial membrane, the cytoplasmic membranes of bacteria and the photosynthetic thylakoid membranes that are found in the chloroplasts of plants; these comprise the so-called ‘energy-conserving’ membranes. Part 1 of this book focuses on fundamental bioenergetic principles. In Part 2, we review our current understanding of the molecular (and increasingly atomic) structure and mechanisms of the protein complexes catalysing these processes, whereas in Part 3 we cover the explosive growth of mammalian cellular bioenergetics, in which the knowledge gained through the study of bioenergetics has become centre stage in investigations of the physiology and pathology of the eukaryotic cell. ‘Bioenergetics’ originated in the quest to understand how oxidation reactions, in the form of the passage of electrons through coenzymes and proteins associated with these energy-conserving membranes, as well as photon capture in photosynthetic systems, could be coupled to the synthesis of ATP, the dominant common energy currency of the cell. The close similarity between the mechanisms and components involved in oxidative and photophosphorylation, as these processes are known respectively, allows them to be studied together. Attempts to relate the mechanism of oxidative phosphorylation to the ATP synthesising reactions in the glycolytic pathway were unsuccessful, and it turned out that this coupling was achieved via ion gradients across membranes in what became known as the chemiosmotic mechanism. It has further emerged over the years that these ion gradients, and hence the chemiosmotic mechanism, explain the coupling between a variety of other processes in cells, including how various species, from sugars and metabolites to proteins, are moved across these membranes (Figure I.1). The fundamentals of the chemiosmotic mechanism are frequently still confused today, 50
2 Introduction to Part 1
Figure I.1 Pathways of energy transduction. The protonmotive force, Δp, interconnects multiple forms of energy. Numbers in square brackets refer to chapters in which pathways are discussed.
years after the emergence of the theory. One of our aims here, in the fourth edition of this book, is to continue to explain what this theory really implies as opposed to the oversimplified and frequently misleading accounts that can be found in many textbooks. The basic principles are wonderfully simple; indeed, the ‘electrical circuit’ analogy we emphasise, with its ‘voltage’ and ‘current’ terms, continues to be useful at a research level. We continue to emphasise the importance of understanding the basic principles of thermodynamics applied to bioenergetic systems. We cover these in Chapter 3. It must be remembered that although thermodynamics can never prove a mechanism, it is ruthless in disproving energetically impossible ones. Particularly in the context of cellular bioenergetics, failure to grasp these key concepts is still disturbingly common. A word of caution, however: the treatment of thermodynamics in Chapter 3 is somewhat unconventional. Students preparing for examinations should check with their lecturers whether to adopt this simpler and more logical system, or to retain the classical approach based on ‘standard states’ and ‘standard free energies’.
Because all biochemical reactions involve energy changes, the term bioenergetics could validly be applied to the whole of life sciences. However, in the field of biochemistry and biology, the term originally came to mean the study of the energy conversion processes that occur on, in, or across the inner mitochondrial membrane, the cytoplasmic membranes of bacteria and the photosynthetic thylakoid membranes that are found in the chloroplasts of plants; these comprise the so-called ‘energy-conserving’ membranes. Part 1 of this book focuses on fundamental bioenergetic principles. In Part 2, we review our current understanding of the molecular (and increasingly atomic) structure and mechanisms of the protein complexes catalysing these processes, whereas in Part 3 we cover the explosive growth of mammalian cellular bioenergetics, in which the knowledge gained through the study of bioenergetics has become centre stage in investigations of the physiology and pathology of the eukaryotic cell. ‘Bioenergetics’ originated in the quest to understand how oxidation reactions, in the form of the passage of electrons through coenzymes and proteins associated with these energy-conserving membranes, as well as photon capture in photosynthetic systems, could be coupled to the synthesis of ATP, the dominant common energy currency of the cell. The close similarity between the mechanisms and components involved in oxidative and photophosphorylation, as these processes are known respectively, allows them to be studied together. Attempts to relate the mechanism of oxidative phosphorylation to the ATP synthesising reactions in the glycolytic pathway were unsuccessful, and it turned out that this coupling was achieved via ion gradients across membranes in what became known as the chemiosmotic mechanism. It has further emerged over the years that these ion gradients, and hence the chemiosmotic mechanism, explain the coupling between a variety of other processes in cells, including how various species, from sugars and metabolites to proteins, are moved across these membranes (Figure I.1). The fundamentals of the chemiosmotic mechanism are frequently still confused today, 50
2 Introduction to Part 1
Figure I.1 Pathways of energy transduction. The protonmotive force, Δp, interconnects multiple forms of energy. Numbers in square brackets refer to chapters in which pathways are discussed.
years after the emergence of the theory. One of our aims here, in the fourth edition of this book, is to continue to explain what this theory really implies as opposed to the oversimplified and frequently misleading accounts that can be found in many textbooks. The basic principles are wonderfully simple; indeed, the ‘electrical circuit’ analogy we emphasise, with its ‘voltage’ and ‘current’ terms, continues to be useful at a research level. We continue to emphasise the importance of understanding the basic principles of thermodynamics applied to bioenergetic systems. We cover these in Chapter 3. It must be remembered that although thermodynamics can never prove a mechanism, it is ruthless in disproving energetically impossible ones. Particularly in the context of cellular bioenergetics, failure to grasp these key concepts is still disturbingly common. A word of caution, however: the treatment of thermodynamics in Chapter 3 is somewhat unconventional. Students preparing for examinations should check with their lecturers whether to adopt this simpler and more logical system, or to retain the classical approach based on ‘standard states’ and ‘standard free energies’.